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Appendix A: OpenMP-HDF5 Programs
-------------------------------------------------------------------------
Program 1
-------------------------------------------------------------------------
/*
* This example writes 64 datasets to a HDF5 file, using multiple threads
* (OpenMP). Each thread grab the lock while it tries to call HDF5 functions
* to write out dataset. In this way, the HDF5 calls are serialized, while
* the calculation part is in parallel. This is one of the ways to do
* OpenMP computation with HDF. As long as not to do HDF I/O in parallel,
* it is safe to use HDF.
*/
#include <hdf5.h>
#include <omp.h>
#include <math.h>
#define NUM_THREADS 4
#define NUM_MDSET 16
#define FILE "SDS.h5"
#define NX 5 /* dataset dimensions */
#define NY 18
#define RANK 2
void CalcWriteData(hid_t, hid_t, hid_t);
/*Global variable, OpenMP lock*/
omp_lock_t lock;
int
main (void)
{
hid_t fid; /* file and dataset handles */
hid_t datatype, dataspace; /* handles */
hsize_t dimsf[2]; /* dataset dimensions */
herr_t status;
int i;
/*
* Create a new file using H5F_ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
*/
fid = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Describe the size of the array and create the data space for fixed
* size dataset.
*/
dimsf[0] = NX;
dimsf[1] = NY;
dataspace = H5Screate_simple(RANK, dimsf, NULL);
/*
* Define datatype for the data in the file.
* We will store little endian INT numbers.
*/
datatype = H5Tcopy(H5T_NATIVE_DOUBLE);
status = H5Tset_order(datatype, H5T_ORDER_LE);
/*Disable dynamic allocation of threads*/
omp_set_dynamic(0);
/*Allocate threads*/
omp_set_num_threads(NUM_THREADS);
/*Initialize lock*/
omp_init_lock(&lock);
/*Each thread grab one iteration in the for loop and call function
* CaclWriteData*/
#pragma omp parallel default(shared)
{
#pragma omp for
for(i=0; i<NUM_THREADS; i++) {
CalcWriteData(fid, dataspace, datatype);
}
}
/*Finished lock mechanism, destroy it*/
omp_destroy_lock(&lock);
/*
* Close/release resources.
*/
H5Sclose(dataspace);
H5Tclose(datatype);
H5Fclose(fid);
return 0;
}
/*Each thread will call this function independantly. They calculate dataset
*and then write it out to hdf, for NUM_MDSET times */
void CalcWriteData(hid_t fid, hid_t dataspace, hid_t datatype)
{
double data[NX][NY];
hid_t dataset;
char dname[16];
int tid;
int i, j, k;
tid = omp_get_thread_num();
for(i=0; i<NUM_MDSET; i++) {
/*Weird calculation to extend computing time*/
for(j=0; j<NX; j++) {
for(k=0; k<NY; k++)
data[j][k] = ( pow(sin(tid), 2.0) + pow(cos(tid), 2.0) ) *
( tid + i ) +
( pow(123456789.0, 8.0) - pow(123456789.0, 8.0) );
}
sprintf(dname, "tid%d-dataset%d", tid, i);
/*Serialize HDF dataset writing using OpenMP lock*/
omp_set_lock(&lock);
dataset = H5Dcreate(fid, dname, datatype, dataspace, H5P_DEFAULT);
H5Dwrite(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT,
data);
H5Dclose(dataset);
/*Release lock*/
omp_unset_lock(&lock);
}
}
-------------------------------------------------------------------------
Program 2
-------------------------------------------------------------------------
/*
* This example compute the element values of an array in parallel
* by two threads. Then write this dataset into HDF file. This is
* one of the ways to do OpenMP computation with HDF. As long as
* not to do HDF I/O in parallel, it is safe to use HDF.
*
*/
#include <hdf5.h>
#include <omp.h>
#define FILE "SDS.h5"
#define DATASETNAME "IntArray"
#define NX 5 /* dataset dimensions */
#define NY 6
#define RANK 2
int
main (void)
{
hid_t file, dataset; /* file and dataset handles */
hid_t datatype, dataspace; /* handles */
hsize_t dimsf[2]; /* dataset dimensions */
herr_t status;
int data[NX][NY]; /* data to write */
int i, j;
/*
* Create a new file using H5F_ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Describe the size of the array and create the data space for fixed
* size dataset.
*/
dimsf[0] = NX;
dimsf[1] = NY;
dataspace = H5Screate_simple(RANK, dimsf, NULL);
/*
* Define datatype for the data in the file.
* We will store little endian INT numbers.
*/
datatype = H5Tcopy(H5T_NATIVE_INT);
status = H5Tset_order(datatype, H5T_ORDER_LE);
/* Disable dynamic allocation of threads. */
omp_set_dynamic(0);
/* Allocate 2 threads */
omp_set_num_threads(2);
/* Parallel computation. Let 2 threads handle this nested for loops
* in parallel. Only one data array is computed. */
#pragma omp parallel default(shared)
{
#pragma omp for
for (j = 0; j < NX; j++) {
#pragma omp parallel shared(j, NY)
{
#pragma omp for
for (i = 0; i < NY; i++)
data[j][i] = i + j;
}
}
}
/* Write this dataset into HDF file */
dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace,
H5P_DEFAULT);
H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
H5Dclose(dataset);
/*
* Close/release resources.
*/
H5Sclose(dataspace);
H5Tclose(datatype);
H5Fclose(file);
return 0;
}
-------------------------------------------------------------------------
Program 3
-------------------------------------------------------------------------
/*
* This example create two threads. Each thread writes a dataset to
* the HDF5 file in parallel. This program only works occasionally.
*/
#include <hdf5.h>
#include <omp.h>
#define FILE "SDS.h5"
#define NX 5 /* dataset dimensions */
#define NY 6
#define RANK 2
void writeData(int, hid_t, hid_t, hid_t, char*);
int main (void)
{
hid_t file; /* file and dataset handles */
hid_t datatype, dataspace; /* handles */
hsize_t dimsf[2]; /* dataset dimensions */
herr_t status;
int id;
char dname[2][10] = {"Array1", "Array2"};
/*
* Create a new file using H5F_ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Describe the size of the array and create the data space for fixed
* size dataset.
*/
dimsf[0] = NX;
dimsf[1] = NY;
dataspace = H5Screate_simple(RANK, dimsf, NULL);
/*
* Define datatype for the data in the file.
* We will store little endian INT numbers.
*/
datatype = H5Tcopy(H5T_NATIVE_INT);
status = H5Tset_order(datatype, H5T_ORDER_LE);
/*Disable dynamic allocation of threads*/
omp_set_dynamic(0);
/*Allocate 2 threads*/
omp_set_num_threads(2);
/*Parallel Part: each thread call function writeData; id is private to
* thread while others are shared */
#pragma omp parallel shared(file, dataspace, datatype, dname) private(id)
{
id = omp_get_thread_num();
writeData(id, file, dataspace, datatype, dname[id]);
}
/*
* Close/release resources.
*/
H5Sclose(dataspace);
H5Tclose(datatype);
H5Fclose(file);
return 0;
}
/*Each thread call this function to write a dataset into HDF5 file*/
void writeData(int id, hid_t file, hid_t dataspace, hid_t datatype, char *dname)
{
int data[NX][NY];
hid_t dataset;
int i, j;
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = i + j + id;
}
dataset = H5Dcreate(file, dname, datatype, dataspace,
H5P_DEFAULT);
H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
H5Dclose(dataset);
}
-------------------------------------------------------------------------
Program 4
-------------------------------------------------------------------------
/*
* This example compute and write two datasets into HDF file in
* parallel. It also only works occasionally.
*/
#include <hdf5.h>
#include <omp.h>
#define FILE "SDS.h5"
#define DATASETNAME "IntArray"
#define NX 5 /* dataset dimensions */
#define NY 6
#define RANK 2
int
main (void)
{
hid_t file, dataset; /* file and dataset handles */
hid_t datatype, dataspace; /* handles */
hsize_t dimsf[2]; /* dataset dimensions */
herr_t status;
int data[NX][NY]; /* data to write */
int i, j, id;
char dname[2][10] = {"intArray1", "intArray2"};
/*
* Create a new file using H5F_ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Describe the size of the array and create the data space for fixed
* size dataset.
*/
dimsf[0] = NX;
dimsf[1] = NY;
dataspace = H5Screate_simple(RANK, dimsf, NULL);
/*
* Define datatype for the data in the file.
* We will store little endian INT numbers.
*/
datatype = H5Tcopy(H5T_NATIVE_INT);
status = H5Tset_order(datatype, H5T_ORDER_LE);
omp_set_dynamic(0);
omp_set_num_threads(2);
/* This part of program compute and write two datasets in parallel. */
#pragma omp parallel shared(file, datatype, dataspace, dname) private(id, j, i, data, dataset)
{
id = omp_get_thread_num();
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = i + j + id;
}
dataset = H5Dcreate(file, dname[id], datatype, dataspace,
H5P_DEFAULT);
H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
H5Dclose(dataset);
}
/*
* Close/release resources.
*/
H5Sclose(dataspace);
H5Tclose(datatype);
H5Fclose(file);
return 0;
}
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